Fix: Convert bcf_annotations.tbi from empty() to value channel to pre…

…vent stalling (#1624) Fixes #1622 --------- Co-authored-by: Friederike Hanssen <[email protected]> Co-authored-by: FriederikeHanssen <[email protected]>
nf-core · Nov 17, 2024 · 0f66cc2 · 0f66cc2
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [1624](https://github.com/nf-core/sarek/pull/1624) - Fix channel stalling for bcftools index
 - [1657](https://github.com/nf-core/sarek/pull/1657) - Update all actions used in the GHA CI
 - [1661](https://github.com/nf-core/sarek/pull/1661) - nf-test pipeline level tests
 - [1673](https://github.com/nf-core/sarek/pull/1673) - Print warning message instead of silent error with Nextflow versions prior to 24.08.0edge

diff --git a/main.nf b/main.nf
@@ -176,7 +176,7 @@ workflow NFCORE_SAREK {
     rt_file                = PREPARE_GENOME.out.rt_file
 
     // Tabix indexed vcf files
-    bcftools_annotations_tbi  = params.bcftools_annotations    ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty([])
+    bcftools_annotations_tbi  = params.bcftools_annotations    ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.value([])
     dbsnp_tbi                 = params.dbsnp                   ? params.dbsnp_tbi                ? Channel.fromPath(params.dbsnp_tbi).collect()                : PREPARE_GENOME.out.dbsnp_tbi                : Channel.value([])
     germline_resource_tbi     = params.germline_resource       ? params.germline_resource_tbi    ? Channel.fromPath(params.germline_resource_tbi).collect()    : PREPARE_GENOME.out.germline_resource_tbi    : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries
     known_indels_tbi          = params.known_indels            ? params.known_indels_tbi         ? Channel.fromPath(params.known_indels_tbi).collect()         : PREPARE_GENOME.out.known_indels_tbi         : Channel.value([])

diff --git a/tests/variant_calling_strelka.nf.test.snap b/tests/variant_calling_strelka.nf.test.snap
@@ -160,7 +160,6 @@
                 "multiqc_bcftools_stats.txt:md5,b2bbb90ef05598e1a70cf36be416c3e2",
                 "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
                 "vcftools_tstv_by_count.txt:md5,d4fdc9722fec46722bda2d04be6801d0",
-                "vcftools_tstv_by_qual.txt:md5,03c5d703ba275136e3b5e2c98488dacc",
                 "sample1.strelka.variants.bcftools_stats.txt:md5,2936f10f99295fb772d8c35f246e223d",
                 "sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt:md5,1c57e5cd6424157536276002ef1a58d6",
                 "sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt:md5,8cf6d0b3f41436cd2f2aa09c9831764d",
@@ -190,23 +189,20 @@
                 "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample1.strelka.variants.FILTER.summary:md5,fef8aeadd3b0f3b8c040c0da03bf1cbd",
                 "sample1.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49",
-                "sample1.strelka.variants.TsTv.qual:md5,f01534408c3a87893b523de5f39deb0b",
                 "sample4_vs_sample3.strelka.somatic_indels.FILTER.summary:md5,30a45e2bc87f40c89388032cbf75ec65",
                 "sample4_vs_sample3.strelka.somatic_indels.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f",
-                "sample4_vs_sample3.strelka.somatic_indels.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883",
                 "sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary:md5,4fc17fa5625b4d1dcc5d791b1eb22d85",
-                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,fc7af1f534890c4ad3025588b3af62ae",
-                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual:md5,75af7d1b1e5a2f1bdfe5b530e37a6cbb"
+                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,fc7af1f534890c4ad3025588b3af62ae"
             ],
             [
-
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-29T14:23:36.950134"
+        "timestamp": "2024-11-15T22:22:40.803241819"
     },
     "Run with profile test | --tools strelka --no_intervals | somatic": {
         "content": [
@@ -356,7 +352,6 @@
                 "multiqc_bcftools_stats.txt:md5,e47ab6f334efa3a95dbd609a27711375",
                 "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
                 "vcftools_tstv_by_count.txt:md5,4244903e90d55bc6cd0cb9f6efcd8a80",
-                "vcftools_tstv_by_qual.txt:md5,d13e0d82e6a0c3dedd712dbd29c878f5",
                 "sample3.strelka.variants.bcftools_stats.txt:md5,c75a458b1aa0e1bae3b667d48684e13c",
                 "sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt:md5,1c57e5cd6424157536276002ef1a58d6",
                 "sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt:md5,110810e5702ef11bc002bd0948dbdfff",
@@ -374,23 +369,20 @@
                 "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample3.strelka.variants.FILTER.summary:md5,8697a0a983314e98b99b5f6038af65f6",
                 "sample3.strelka.variants.TsTv.count:md5,1481854d2a765f5641856ecf95ca4097",
-                "sample3.strelka.variants.TsTv.qual:md5,fd8e449a715922e24fe4ea9c89870432",
                 "sample4_vs_sample3.strelka.somatic_indels.FILTER.summary:md5,30a45e2bc87f40c89388032cbf75ec65",
                 "sample4_vs_sample3.strelka.somatic_indels.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f",
-                "sample4_vs_sample3.strelka.somatic_indels.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883",
                 "sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary:md5,7a81b11aa29fec73d5bc872b7b58f8aa",
-                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,a922c51ca3b2ea7cdcfa09e9c8c55d52",
-                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual:md5,75af7d1b1e5a2f1bdfe5b530e37a6cbb"
+                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,a922c51ca3b2ea7cdcfa09e9c8c55d52"
             ],
             [
-
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-29T14:31:34.94648"
+        "timestamp": "2024-11-15T22:29:05.475529758"
     },
     "Run with profile test | --tools strelka | somatic": {
         "content": [
@@ -537,7 +529,6 @@
                 "multiqc_bcftools_stats.txt:md5,c2674bda60d8fa805601c436afe16f18",
                 "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
                 "vcftools_tstv_by_count.txt:md5,3888b9a69fdeaf6667dcc600ff776413",
-                "vcftools_tstv_by_qual.txt:md5,e10ee9b12add8443d3bc98d04733140a",
                 "sample3.strelka.variants.bcftools_stats.txt:md5,d505d381e8c3906788e4135bb975ff84",
                 "sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt:md5,1c57e5cd6424157536276002ef1a58d6",
                 "sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt:md5,8cf6d0b3f41436cd2f2aa09c9831764d",
@@ -555,23 +546,20 @@
                 "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample3.strelka.variants.FILTER.summary:md5,fef8aeadd3b0f3b8c040c0da03bf1cbd",
                 "sample3.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49",
-                "sample3.strelka.variants.TsTv.qual:md5,f01534408c3a87893b523de5f39deb0b",
                 "sample4_vs_sample3.strelka.somatic_indels.FILTER.summary:md5,30a45e2bc87f40c89388032cbf75ec65",
                 "sample4_vs_sample3.strelka.somatic_indels.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f",
-                "sample4_vs_sample3.strelka.somatic_indels.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883",
                 "sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary:md5,4fc17fa5625b4d1dcc5d791b1eb22d85",
-                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,fc7af1f534890c4ad3025588b3af62ae",
-                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual:md5,75af7d1b1e5a2f1bdfe5b530e37a6cbb"
+                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,fc7af1f534890c4ad3025588b3af62ae"
             ],
             [
-
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-29T14:29:18.353277"
+        "timestamp": "2024-11-15T22:27:18.76415046"
     },
     "Run with profile test | --tools strelka | germline": {
         "content": [
@@ -687,7 +675,6 @@
                 "multiqc_bcftools_stats.txt:md5,cde557db5eb46f8325c06e9bb32e7a94",
                 "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
                 "vcftools_tstv_by_count.txt:md5,69cbd9060c01c1102ddf5839ee7b404a",
-                "vcftools_tstv_by_qual.txt:md5,6973bf3d8488aa52d64933412f0556df",
                 "sample1.strelka.variants.bcftools_stats.txt:md5,2936f10f99295fb772d8c35f246e223d",
                 "sample1.recal.mosdepth.global.dist.txt:md5,d9a4dd6429560b2b647da346050766c5",
                 "sample1.recal.mosdepth.region.dist.txt:md5,1f3dab381958e08eb00f7c5e1135f677",
@@ -696,18 +683,17 @@
                 "sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
                 "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
                 "sample1.strelka.variants.FILTER.summary:md5,fef8aeadd3b0f3b8c040c0da03bf1cbd",
-                "sample1.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49",
-                "sample1.strelka.variants.TsTv.qual:md5,f01534408c3a87893b523de5f39deb0b"
+                "sample1.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49"
             ],
             [
-
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-29T14:25:18.773706"
+        "timestamp": "2024-11-15T22:24:13.636617483"
     },
     "Run with profile test | --tools strelka --no_intervals | germline": {
         "content": [
@@ -826,7 +812,6 @@
                 "multiqc_bcftools_stats.txt:md5,23c19e033f3086bec87c5e2022795e79",
                 "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
                 "vcftools_tstv_by_count.txt:md5,ea99842f730543b5fd1a08d0e1d68278",
-                "vcftools_tstv_by_qual.txt:md5,a603c008a52ffd0297aa420743fbdc8d",
                 "sample1.strelka.variants.bcftools_stats.txt:md5,0e829f5d31d768a8e99786786282c9ef",
                 "sample1.recal.mosdepth.global.dist.txt:md5,d9a4dd6429560b2b647da346050766c5",
                 "sample1.recal.mosdepth.region.dist.txt:md5,1f3dab381958e08eb00f7c5e1135f677",
@@ -835,17 +820,16 @@
                 "sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
                 "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
                 "sample1.strelka.variants.FILTER.summary:md5,8697a0a983314e98b99b5f6038af65f6",
-                "sample1.strelka.variants.TsTv.count:md5,1481854d2a765f5641856ecf95ca4097",
-                "sample1.strelka.variants.TsTv.qual:md5,fd8e449a715922e24fe4ea9c89870432"
+                "sample1.strelka.variants.TsTv.count:md5,1481854d2a765f5641856ecf95ca4097"
             ],
             [
-
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-29T14:27:06.859001"
+        "timestamp": "2024-11-15T22:25:42.940353635"
     }
-}
+}
diff --git a/tests/variant_calling_strelka_bp.nf.test.snap b/tests/variant_calling_strelka_bp.nf.test.snap
@@ -180,7 +180,6 @@
                 "multiqc_bcftools_stats.txt:md5,5c9c75a7ba51eec6d7ed539a5d0a2397",
                 "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
                 "vcftools_tstv_by_count.txt:md5,d5919b93082809cb0663b16ce1f0f60e",
-                "vcftools_tstv_by_qual.txt:md5,ad9f0e77ff15fb86ddad62e088389e26",
                 "sample3.manta.diploid_sv.bcftools_stats.txt:md5,8adad91e1c8dc8db63cf9b3607bee3a0",
                 "sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt:md5,17dc847445b98885bc18622f862f44d9",
                 "sample4_vs_sample3.manta.somatic_sv.bcftools_stats.txt:md5,a8660b352950f0b32768fcbbd6b48896",
@@ -201,32 +200,26 @@
                 "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample3.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
-                "sample3.manta.diploid_sv.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883",
                 "sample4_vs_sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample4_vs_sample3.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
-                "sample4_vs_sample3.manta.diploid_sv.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883",
                 "sample4_vs_sample3.manta.somatic_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample4_vs_sample3.manta.somatic_sv.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f",
-                "sample4_vs_sample3.manta.somatic_sv.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883",
                 "sample3.strelka.variants.FILTER.summary:md5,8697a0a983314e98b99b5f6038af65f6",
                 "sample3.strelka.variants.TsTv.count:md5,1481854d2a765f5641856ecf95ca4097",
-                "sample3.strelka.variants.TsTv.qual:md5,fd8e449a715922e24fe4ea9c89870432",
                 "sample4_vs_sample3.strelka.somatic_indels.FILTER.summary:md5,30a45e2bc87f40c89388032cbf75ec65",
                 "sample4_vs_sample3.strelka.somatic_indels.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f",
-                "sample4_vs_sample3.strelka.somatic_indels.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883",
                 "sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary:md5,7a81b11aa29fec73d5bc872b7b58f8aa",
-                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,a922c51ca3b2ea7cdcfa09e9c8c55d52",
-                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual:md5,75af7d1b1e5a2f1bdfe5b530e37a6cbb"
+                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,a922c51ca3b2ea7cdcfa09e9c8c55d52"
             ],
             [
-
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-29T14:39:02.340325"
+        "timestamp": "2024-11-15T22:39:15.50268779"
     },
     "Run with profile test | --tools manta,strelka | somatic": {
         "content": [
@@ -406,7 +399,6 @@
                 "multiqc_bcftools_stats.txt:md5,97bac5dbfe6cb21a78ca7f7327655b65",
                 "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
                 "vcftools_tstv_by_count.txt:md5,27388870c36896df470e2f5aa982332e",
-                "vcftools_tstv_by_qual.txt:md5,7b7b2f5ce5b9d129a7e3d775de29b9b1",
                 "sample3.manta.diploid_sv.bcftools_stats.txt:md5,8adad91e1c8dc8db63cf9b3607bee3a0",
                 "sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt:md5,17dc847445b98885bc18622f862f44d9",
                 "sample4_vs_sample3.manta.somatic_sv.bcftools_stats.txt:md5,a8660b352950f0b32768fcbbd6b48896",
@@ -427,31 +419,25 @@
                 "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample3.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
-                "sample3.manta.diploid_sv.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883",
                 "sample4_vs_sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample4_vs_sample3.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
-                "sample4_vs_sample3.manta.diploid_sv.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883",
                 "sample4_vs_sample3.manta.somatic_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample4_vs_sample3.manta.somatic_sv.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f",
-                "sample4_vs_sample3.manta.somatic_sv.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883",
                 "sample3.strelka.variants.FILTER.summary:md5,fef8aeadd3b0f3b8c040c0da03bf1cbd",
                 "sample3.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49",
-                "sample3.strelka.variants.TsTv.qual:md5,f01534408c3a87893b523de5f39deb0b",
                 "sample4_vs_sample3.strelka.somatic_indels.FILTER.summary:md5,30a45e2bc87f40c89388032cbf75ec65",
                 "sample4_vs_sample3.strelka.somatic_indels.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f",
-                "sample4_vs_sample3.strelka.somatic_indels.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883",
                 "sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary:md5,4fc17fa5625b4d1dcc5d791b1eb22d85",
-                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,fc7af1f534890c4ad3025588b3af62ae",
-                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual:md5,75af7d1b1e5a2f1bdfe5b530e37a6cbb"
+                "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,fc7af1f534890c4ad3025588b3af62ae"
             ],
             [
-
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-29T14:36:40.89285"
+        "timestamp": "2024-11-15T22:37:23.231917992"
     }
-}
+}